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| Status |
Public on Sep 07, 2021 |
| Title |
Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta |
| Organisms |
Macaca fascicularis; Macaca mulatta |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
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| Summary |
Our knowledge of genomic imprinting in primates is lagging behand that of mice largely due to the difficulties of allelic analyses in outbred animals. To understand imprinting dynamics in primates, we profiled transcriptomes, DNA methylomes and H3K27me3 in uniparental monkey embryos. We further developed single-nucleotide polymorphisms (SNP)-free methods, TARSII and CARSII, to identify germline differentially methylated regions (DMRs) in somatic tissues. Our comprehensive analyses showed that allelic DNA methylation, but not H3K27me3, is a major mark that correlates with paternal-biasedly expressed genes (PEGs) in uniparental monkey embryos. Interestingly, primate germline DMRs are different from PEG-associated DMRs in early embryos and are enriched in placenta. Strikingly, most placenta-specific germline DMRs are lost in placenta of cloned monkey. Collectively, our study establishes SNP-free germline DMR identification methods, defines developmental imprinting dynamics in primates and demonstrates imprinting defects in cloned monkey placenta, which provides important clues for improving primate cloning.
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| Overall design |
We conducted RNA-seq, H3K27me3 CUT&RUN and WGBS in monkey uniparental 16-cell embryos. Also we have profiled WGBS in monkey adult tissues, WGBS and RNA-seq in monkey wild-type and SCNT placenta.
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| Contributor(s) |
Chu C, Zhang W, Kang Y, Ji W, Niu Y, Zhang Y |
| Citation(s) |
34619096 |
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| Submission date |
Oct 10, 2020 |
| Last update date |
Oct 12, 2021 |
| Contact name |
Wenhao Zhang |
| E-mail(s) |
zwhonep2@gmail.com
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| Phone |
+1 617-784-1683
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| Organization name |
Harvard Medical School
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| Department |
Genetics
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| Lab |
Yi Zhang
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| Street address |
Warren Alpert Bldg, Rm 160, 200 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (2) |
| GPL19129 |
Illumina HiSeq 2500 (Macaca mulatta) |
| GPL20302 |
Illumina HiSeq 2500 (Macaca fascicularis) |
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| Samples (29)
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| Relations |
| BioProject |
PRJNA668521 |
| SRA |
SRP286979 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE159347_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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